Table 1.
Overview of metabolic models and general polyhedra used for performance tests and comparisons of efmtool [12] and mplrs [1]. For metabolic models the number of rows corresponds to the number of metabolites and the number of columns to the number of reactions with numbers in brackets referring to the number of reversible reactions. For the metabolic models the dimensions of the original uncompressed model and a comparison between the compressions of efmtool and EFMlrs are given. For the polytopes, the matrix dimensions of the original uncompressed (uncmp.) polytope P, the transformed uncompressed and via efmtool compressed model in the flux cone FC are shown. All polytopes were obtained from the lrs homepage [27]. comp., compression; Deg., degree of degeneracy
| Model | uncmp. P | uncmp. FC | efmtool comp. | EFMIrs comp. | EFMs | Deg. | ||||
|---|---|---|---|---|---|---|---|---|---|---|
| Columns | Rows | Columns | Rows | Columns | Rows | Columns | Rows | |||
| EColiCentral [28] | 71 (15) | 53 | 44 (11) | 26 | 44 (11) | 21 | 429,276 | High | ||
| EColiCore2 [29] | 82 (22) | 54 | 58 (18) | 30 | 58 (18) | 30 | 34,896,477 | High | ||
| iPS189 [30] | 277 (21) | 271 | 67 (13) | 42 | 63 (13) | 35 | 3,252,686 | High | ||
| JCVI-syn3A [31] | 316 (8) | 286 | 100 (7) | 50 | 100 (7) | 48 | ? | High | ||
| cp6 [27] | 16 (15) | 368 | 384 (15) | 368 | 384 (15) | 368 | 32 | High | ||
| bv7 [27] | 57 (56) | 69 | 106 (56) | 69 | 49 (0) | 12 | 5,040 | High | ||
| mit71 [27] | 61 (60) | 71 | 132 (60) | 71 | 132 (60) | 71 | 3,149,579 | Moderate | ||
| fq48-19 [27] | 19 (18) | 48 | 67 (18) | 48 | 48 (0) | 29 | 119,184 | Moderate | ||
| mit [27] | 9 (8) | 729 | 738 (8) | 729 | 729 (0) | 720 | 4,862 | Moderate | ||
| perm10 [27] | 11 (10) | 1023 | 1033 (10) | 1023 | 1033 (10) | 1023 | 3628800 | Simple | ||